Variant report

Variant	rs3795134
Chromosome Location	chr20:1447941-1447942
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr20:1446710-1447988	HepG2	liver:	n/a	n/a
2	GTF2F1	chr20:1447333-1448934	K562	blood:	n/a	n/a
3	CTCF	chr20:1446644-1448611	A549	lung:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
4	EP300	chr20:1447067-1448184	HepG2	liver:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
5	SP4	chr20:1447337-1448015	H1-hESC	embryonic stem cell:	n/a	chr20:1447596-1447607
6	SMC3	chr20:1447500-1448649	HepG2	liver:	n/a	chr20:1447655-1447669
7	CTCF	chr20:1447301-1447969	HCT-116	colon:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
8	CBX3	chr20:1447112-1447964	HCT-116	colon:	n/a	n/a
9	MXI1	chr20:1446807-1448702	HepG2	liver:	n/a	n/a
10	CTCF	chr20:1447920-1448070	SK-N-SH_RA	brain:	n/a	n/a
11	ARID3A	chr20:1447389-1448758	HepG2	liver:	n/a	chr20:1447465-1447480
12	MAZ	chr20:1446758-1447972	IMR90	lung:	n/a	chr20:1447602-1447611 chr20:1447606-1447613
13	POLR2A	chr20:1447047-1449237	K562	blood:	n/a	n/a
14	POLR2A	chr20:1447018-1449457	NB4	blood:	n/a	n/a
15	SP1	chr20:1447221-1447995	HCT-116	colon:	n/a	chr20:1447724-1447733 chr20:1447597-1447606 chr20:1447717-1447729 chr20:1447597-1447606 chr20:1447596-1447608 chr20:1447596-1447608 chr20:1447719-1447728 chr20:1447597-1447607 chr20:1447598-1447607 chr20:1447596-1447607
16	ZNF143	chr20:1447404-1448872	K562	blood:	n/a	n/a
17	MAFF	chr20:1447104-1448009	HepG2	liver:	n/a	n/a
18	RCOR1	chr20:1447322-1448629	K562	blood:	n/a	n/a
19	POLR2A	chr20:1446816-1449625	HL-60	blood:	n/a	n/a
20	MYBL2	chr20:1446821-1448288	HepG2	liver:	n/a	n/a
21	CTCF	chr20:1447880-1448030	HPAF	blood vessel:	n/a	n/a
22	RCOR1	chr20:1447062-1448324	HepG2	liver:	n/a	n/a
23	BHLHE40	chr20:1447084-1448616	K562	blood:	n/a	chr20:1447494-1447510 chr20:1447574-1447590 chr20:1447087-1447103
24	SRF	chr20:1447036-1447954	HCT-116	colon:	n/a	chr20:1447598-1447608 chr20:1447327-1447337
25	TBP	chr20:1446839-1449132	K562	blood:	n/a	n/a
26	ZNF384	chr20:1447291-1448671	K562	blood:	n/a	n/a
27	RFX5	chr20:1446925-1447947	HepG2	liver:	n/a	n/a
28	EP300	chr20:1446810-1447954	SK-N-SH	brain:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
29	FOSL2	chr20:1447253-1448139	HepG2	liver:	n/a	chr20:1447722-1447731
30	GATA1	chr20:1446696-1448690	PBDE	blood:	n/a	n/a
31	MBD4	chr20:1447268-1448159	HepG2	liver:	n/a	n/a
32	HEY1	chr20:1447278-1448011	HepG2	liver:	n/a	chr20:1447662-1447677 chr20:1447588-1447603 chr20:1447344-1447359
33	MBD4	chr20:1446951-1448473	HepG2	liver:	n/a	n/a
34	GABPA	chr20:1447090-1447979	HL-60	blood:	n/a	chr20:1447535-1447542
35	E2F6	chr20:1447139-1449044	K562	blood:	n/a	chr20:1447465-1447480 chr20:1447305-1447315
36	CHD2	chr20:1446884-1448111	K562	blood:	n/a	n/a
37	TBP	chr20:1447229-1447956	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBL1XR1	chr20:1447333-1448051	K562	blood:	n/a	n/a
39	POLR2A	chr20:1446889-1449085	HL-60	blood:	n/a	n/a
40	ESRRA	chr20:1446868-1448156	GM12878	blood:	n/a	n/a
41	PML	chr20:1446914-1448076	GM12878	blood:	n/a	n/a
42	BRCA1	chr20:1447386-1448276	HepG2	liver:	n/a	n/a
43	POLR2A	chr20:1446204-1448182	IMR90	lung:	n/a	n/a
44	CTCF	chr20:1446616-1448042	SK-N-SH	brain:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
45	USF2	chr20:1447837-1448037	HepG2	liver:	n/a	n/a
46	POLR2A	chr20:1447001-1449309	K562	blood:	n/a	n/a
47	HCFC1	chr20:1447055-1448709	K562	blood:	n/a	n/a
48	EP300	chr20:1447361-1448861	GM12878	blood:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
49	BHLHE40	chr20:1446983-1447944	HepG2	liver:	n/a	chr20:1447494-1447510 chr20:1447574-1447590 chr20:1447087-1447103
50	POLR2A	chr20:1446878-1448580	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1304840..1306676-chr20:1447020..1448985,3	K562	blood:
2	chr20:1306070..1308541-chr20:1446001..1448028,2	MCF-7	breast:
3	chr20:1371233..1373934-chr20:1446935..1449162,2	K562	blood:
4	chr20:1437321..1440209-chr20:1445376..1448458,3	MCF-7	breast:
5	chr20:1372232..1375944-chr20:1446656..1450761,3	MCF-7	breast:
6	chr20:1304611..1307577-chr20:1447050..1450049,5	K562	blood:
7	chr20:1372434..1374768-chr20:1446935..1449052,2	K562	blood:
8	chr20:1436244..1441221-chr20:1444525..1448562,4	MCF-7	breast:

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000088832	Chromatin interaction
ENSG00000234684	Chromatin interaction
ENSG00000088833	Chromatin interaction
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1543423	0.90[JPT][hapmap]
rs3795135	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6033858	0.86[ASN][1000 genomes]
rs6033860	0.85[JPT][hapmap]
rs6033867	0.90[JPT][hapmap]
rs6033901	0.80[JPT][hapmap]
rs6033950	0.80[JPT][hapmap]
rs6042462	0.81[JPT][hapmap]
rs6042592	0.85[JPT][hapmap]
rs6074709	0.80[JPT][hapmap]
rs6074715	0.80[JPT][hapmap]
rs6079294	0.90[JPT][hapmap]
rs6079325	0.80[JPT][hapmap]
rs6079330	0.81[JPT][hapmap]
rs6079336	0.81[JPT][hapmap]
rs6079354	0.81[JPT][hapmap]
rs6079361	0.81[JPT][hapmap]
rs6110207	0.81[JPT][hapmap]
rs6110226	0.85[JPT][hapmap]
rs6135033	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6135060	0.90[JPT][hapmap]
rs6135061	0.85[JPT][hapmap]
rs6135089	0.85[JPT][hapmap]
rs6135095	0.85[JPT][hapmap]
rs963867	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv3375230	chr20:1446177-1448725	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1446200-1448000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr20:1446200-1448000	Active TSS	Fetal Muscle Trunk	muscle
3	chr20:1446600-1448000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr20:1446600-1448000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr20:1446600-1448000	Active TSS	Left Ventricle	heart
6	chr20:1446600-1448000	Active TSS	Psoas Muscle	Psoas
7	chr20:1446600-1448200	Active TSS	Gastric	stomach
8	chr20:1446800-1448000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr20:1446800-1448000	Active TSS	Brain Germinal Matrix	brain
10	chr20:1446800-1448200	Active TSS	Fetal Brain Female	brain
11	chr20:1446800-1448200	Active TSS	Fetal Kidney	kidney
12	chr20:1446800-1448200	Active TSS	Fetal Stomach	stomach
13	chr20:1446800-1448600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr20:1446800-1449000	Active TSS	Brain Hippocampus Middle	brain
15	chr20:1447000-1448000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:1447000-1448000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:1447000-1448000	Active TSS	Fetal Heart	heart
18	chr20:1447000-1448000	Active TSS	Osteobl	bone
19	chr20:1447000-1448400	Active TSS	Rectal Smooth Muscle	rectum
20	chr20:1447200-1448200	Active TSS	Stomach Smooth Muscle	stomach
21	chr20:1447400-1448000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:1447400-1448000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr20:1447600-1448000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr20:1447600-1448000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:1447600-1448000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr20:1447600-1448000	Enhancers	HSMMtube	muscle
27	chr20:1447600-1448200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:1447600-1448200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:1447600-1448200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr20:1447600-1448200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:1447600-1448200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr20:1447600-1448200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr20:1447600-1448200	Enhancers	HMEC	breast
34	chr20:1447600-1448400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:1447600-1448400	Enhancers	Esophagus	oesophagus
36	chr20:1447600-1448600	Enhancers	Lung	lung
37	chr20:1447600-1449000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr20:1447600-1449800	Weak transcription	Small Intestine	intestine
39	chr20:1447600-1450000	Weak transcription	Aorta	Aorta
40	chr20:1447800-1448000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr20:1447800-1448000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
42	chr20:1447800-1448000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:1447800-1448000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr20:1447800-1448000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr20:1447800-1448000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr20:1447800-1448000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr20:1447800-1448000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:1447800-1448000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr20:1447800-1448000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr20:1447800-1448000	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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